# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 02:38:03 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (2R)-4-[2-(2,3-dihydro-1H-indol-1-yl)-2-oxoethyl]-2-methylpiperazin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN(CC[NH2+]1)CC(=O)N2CCc3ccccc23
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 4YE  4YE  (2R)-4-[2-(2,3-dihydro-1H-indol-1-yl)-2-oxoethyl]-2-methylpiperazin-1-ium  ligand  41  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4YE
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 4YE  C1   C  CH3   0  -0.673  -5.2604   1.7820   0.5812
 4YE  C2   C  CH1   0  -0.146  -4.3043   0.6133   0.4805
 4YE  C3   C  CH2   0  -0.267  -2.8509   1.0412   0.3783
 4YE  N4   N  NT    0  -0.422  -1.9788  -0.1079   0.2410
 4YE  C5   C  CH2   0  -0.420  -0.5884   0.2571   0.3341
 4YE  C6   C  C     0   0.530   0.2812  -0.9445   0.6671
 4YE  C10  C  CH2   0  -0.494   3.7395  -1.6737  -0.1633
 4YE  C11  C  CR56  0  -0.020   3.6898  -0.1771  -0.2296
 4YE  C12  C  CR16  0  -0.320   4.6781   0.7149  -0.5917
 4YE  C13  C  CR16  0  -0.262   4.4039   2.0804  -0.5774
 4YE  C14  C  CR16  0  -0.263   3.1498   2.5257  -0.1891
 4YE  C15  C  CR16  0  -0.297   2.1462   1.6341   0.1830
 4YE  C16  C  CR56  0   0.413   2.4202   0.2733   0.1387
 4YE  O7   O  O     0  -0.468  -0.2008  -1.9888   1.0692
 4YE  N8   N  NR5   0  -0.604   1.6216  -0.8319   0.4801
 4YE  C9   C  CH2   0  -0.289   2.4754  -2.0209   0.6255
 4YE  C17  C  CH2   0  -0.310  -2.2849  -0.8370  -0.9739
 4YE  C18  C  CH2   0  -0.324  -3.7058  -1.3478  -0.9297
 4YE  N19  N  NT2   1  -0.648  -4.6413  -0.2075  -0.7269
 4YE  H20  H  HCH3  0   0.263  -6.2950   1.4437   0.6351
 4YE  H22  H  HCH3  0   0.267  -5.0494   2.3463   1.4879
 4YE  H21  H  HCH3  0   0.247  -5.1573   2.4563  -0.2693
 4YE  H23  H  HCH1  0   0.305  -4.4257  -0.0600   1.3300
 4YE  H24  H  HCH2  0   0.222  -2.7399   1.7601  -0.4517
 4YE  H25  H  HCH2  0   0.279  -2.6030   1.5730   1.2977
 4YE  H27  H  HCH2  0   0.252  -0.2197   0.7488  -0.5794
 4YE  H26  H  HCH2  0   0.295  -0.4761   0.9834   1.1448
 4YE  H31  H  HCH2  0   0.269   4.6384  -2.0475   0.3250
 4YE  H32  H  HCR6  0   0.256   5.6583   0.3549  -0.8792
 4YE  H33  H  HCR6  0   0.256   5.1706   2.7912  -0.8561
 4YE  H34  H  HCR6  0   0.260   2.9401   3.5868  -0.1555
 4YE  H35  H  HCR6  0   0.273   1.1996   2.0302   0.5147
 4YE  H28  H  HCH2  0   0.263   1.9661  -2.9009   0.2419
 4YE  H29  H  HCH2  0   0.258   2.6974  -2.1892   1.6815
 4YE  H37  H  HCH2  0   0.232  -2.1390  -0.2181  -1.8753
 4YE  H36  H  HCH2  0   0.283  -1.6318  -1.7032  -1.0688
 4YE  H38  H  HCH2  0   0.308  -3.9842  -1.8394  -1.8583
 4YE  H39  H  HCH2  0   0.296  -3.8547  -2.0342  -0.0988
 4YE  H41  H  HNT2  0   0.477  -5.5963  -0.5596  -0.6498
 4YE  H40  H  HNT2  0   0.460  -4.6384   0.3862  -1.5598
 4YE  H30  H  HCH2  0   0.266   3.7104  -2.1048  -1.1671

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 4YE  C12  C13  aromatic  1.393  0.020  1.393
 4YE  C12  C11  aromatic  1.380  0.020  1.380
 4YE  C13  C14  aromatic  1.386  0.020  1.386
 4YE  C11  C10  single    1.499  0.020  1.499
 4YE  C11  C16  aromatic  1.397  0.020  1.397
 4YE  C10  C9   single    1.530  0.020  1.530
 4YE  C14  C15  aromatic  1.393  0.020  1.393
 4YE  C16  C15  aromatic  1.389  0.020  1.389
 4YE  C16  N8   single    1.406  0.020  1.406
 4YE  C9   N8   single    1.471  0.020  1.471
 4YE  N8   C6   single    1.358  0.020  1.358
 4YE  C6   O7   double    1.218  0.020  1.218
 4YE  C6   C5   single    1.520  0.020  1.520
 4YE  C5   N4   single    1.441  0.020  1.441
 4YE  N4   C3   single    1.449  0.020  1.449
 4YE  N4   C17  single    1.450  0.020  1.450
 4YE  C3   C2   single    1.518  0.020  1.518
 4YE  C17  C18  single    1.511  0.020  1.511
 4YE  C2   C1   single    1.513  0.020  1.513
 4YE  C2   N19  single    1.498  0.020  1.498
 4YE  C18  N19  single    1.489  0.020  1.489
 4YE  C1   H20  single    0.970  0.020  1.090
 4YE  C1   H22  single    0.970  0.020  1.090
 4YE  C1   H21  single    0.970  0.020  1.090
 4YE  C2   H23  single    0.970  0.020  1.090
 4YE  C3   H24  single    0.970  0.020  1.090
 4YE  C3   H25  single    0.970  0.020  1.090
 4YE  C5   H27  single    0.970  0.020  1.090
 4YE  C5   H26  single    0.970  0.020  1.090
 4YE  C10  H30  single    0.970  0.020  1.090
 4YE  C10  H31  single    0.970  0.020  1.090
 4YE  C12  H32  single    0.930  0.020  1.080
 4YE  C13  H33  single    0.930  0.020  1.080
 4YE  C14  H34  single    0.930  0.020  1.080
 4YE  C15  H35  single    0.930  0.020  1.080
 4YE  C9   H28  single    0.970  0.020  1.090
 4YE  C9   H29  single    0.970  0.020  1.090
 4YE  C17  H37  single    0.970  0.020  1.090
 4YE  C17  H36  single    0.970  0.020  1.090
 4YE  C18  H38  single    0.970  0.020  1.090
 4YE  C18  H39  single    0.970  0.020  1.090
 4YE  N19  H41  single    0.890  0.020  1.040
 4YE  N19  H40  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 4YE  H21  C1   H22  108.11  3.000
 4YE  H21  C1   H20  108.68  3.000
 4YE  H22  C1   H20  107.69  3.000
 4YE  H21  C1   C2   111.46  3.000
 4YE  H22  C1   C2   109.47  3.000
 4YE  H20  C1   C2   111.31  3.000
 4YE  H23  C2   N19  105.33  3.000
 4YE  H23  C2   C3   109.44  3.000
 4YE  N19  C2   C3   108.38  3.000
 4YE  H23  C2   C1   110.77  3.000
 4YE  N19  C2   C1   109.55  3.000
 4YE  C3   C2   C1   113.06  3.000
 4YE  H25  C3   H24  107.07  3.000
 4YE  H25  C3   N4   109.25  3.000
 4YE  H24  C3   N4   112.63  3.000
 4YE  H25  C3   C2   107.35  3.000
 4YE  H24  C3   C2   109.29  3.000
 4YE  N4   C3   C2   111.04  3.000
 4YE  C17  N4   C5   112.67  3.000
 4YE  C17  N4   C3   110.56  3.000
 4YE  C5   N4   C3   111.95  3.000
 4YE  H26  C5   H27  106.49  3.000
 4YE  H26  C5   C6   107.68  3.000
 4YE  H27  C5   C6   110.07  3.000
 4YE  H26  C5   N4   108.36  3.000
 4YE  H27  C5   N4   112.51  3.000
 4YE  C6   C5   N4   111.47  3.000
 4YE  N8   C6   O7   120.46  3.000
 4YE  O7   C6   C5   121.57  3.000
 4YE  N8   C6   C5   117.96  3.000
 4YE  H31  C10  H30  107.36  3.000
 4YE  H31  C10  C9   111.89  3.000
 4YE  H30  C10  C9   111.22  3.000
 4YE  H31  C10  C11  112.95  3.000
 4YE  H30  C10  C11  110.64  3.000
 4YE  C9   C10  C11  102.82  3.000
 4YE  C16  C11  C12  120.79  3.000
 4YE  C16  C11  C10  109.91  3.000
 4YE  C12  C11  C10  129.30  3.000
 4YE  H32  C12  C13  120.45  3.000
 4YE  H32  C12  C11  120.21  3.000
 4YE  C13  C12  C11  119.35  3.000
 4YE  H33  C13  C14  120.14  3.000
 4YE  H33  C13  C12  120.12  3.000
 4YE  C14  C13  C12  119.73  3.000
 4YE  H34  C14  C15  118.66  3.000
 4YE  H34  C14  C13  119.93  3.000
 4YE  C15  C14  C13  121.40  3.000
 4YE  H35  C15  C16  122.88  3.000
 4YE  H35  C15  C14  118.65  3.000
 4YE  C16  C15  C14  118.45  3.000
 4YE  N8   C16  C15  130.58  3.000
 4YE  N8   C16  C11  109.08  3.000
 4YE  C15  C16  C11  120.25  3.000
 4YE  C9   N8   C16  109.26  3.000
 4YE  C9   N8   C6   119.48  3.000
 4YE  C16  N8   C6   131.26  3.000
 4YE  H29  C9   H28  108.17  3.000
 4YE  H29  C9   N8   109.76  3.000
 4YE  H28  C9   N8   110.35  3.000
 4YE  H29  C9   C10  111.44  3.000
 4YE  H28  C9   C10  112.89  3.000
 4YE  N8   C9   C10  104.19  3.000
 4YE  H36  C17  H37  107.21  3.000
 4YE  H36  C17  C18  107.32  3.000
 4YE  H37  C17  C18  109.76  3.000
 4YE  H36  C17  N4   110.27  3.000
 4YE  H37  C17  N4   112.01  3.000
 4YE  C18  C17  N4   110.13  3.000
 4YE  H39  C18  H38  109.40  3.000
 4YE  H39  C18  N19  107.06  3.000
 4YE  H38  C18  N19  107.57  3.000
 4YE  H39  C18  C17  111.37  3.000
 4YE  H38  C18  C17  111.64  3.000
 4YE  N19  C18  C17  109.63  3.000
 4YE  H40  N19  H41  105.33  3.000
 4YE  H40  N19  C18  109.39  3.000
 4YE  H41  N19  C18  109.51  3.000
 4YE  H40  N19  C2   109.73  3.000
 4YE  H41  N19  C2   109.78  3.000
 4YE  C18  N19  C2   112.83  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 4YE  CONST_01  C14  C13  C12  C11    0.00   0.0  0
 4YE  CONST_02  C14  C15  C16  C11    0.00   0.0  0
 4YE  CONST_03  C15  C14  C13  C12    0.00   0.0  0
 4YE  CONST_04  C15  C16  C11  C12    0.00   0.0  0
 4YE  CONST_05  C16  C11  C12  C13    0.00   0.0  0
 4YE  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 4YE  CONST_07  H32  C12  C11  C10    0.00   0.0  0
 4YE  CONST_08  H33  C13  C12  C11  180.00   0.0  0
 4YE  CONST_09  H35  C15  C16  C11  180.00   0.0  0
 4YE  CONST_10  H34  C14  C13  C12  180.00   0.0  0
 4YE  CONST_11  C16  N8   C6   C5     0.00   0.0  0
 4YE  CONST_12  C9   N8   C6   C5   180.00   0.0  0
 4YE  CONST_13  O7   C6   N8   C16  180.00   0.0  0
 4YE  CONST_14  C9   N8   C6   O7     0.00   0.0  0
 4YE  Var_01    C17  N4   C3   C2    61.77  30.0  1
 4YE  Var_02    C17  C18  N19  C2   -54.55  30.0  1
 4YE  Var_03    C18  C17  N4   C3   -61.35  30.0  1
 4YE  Var_04    N19  C18  C17  N4    56.95  30.0  1
 4YE  Var_05    C16  N8   C9   C10  -21.09  30.0  1
 4YE  Var_06    N8   C9   C10  C11   20.55  30.0  1
 4YE  Var_07    C9   N8   C16  C11   12.77  30.0  1
 4YE  Var_08    C9   C10  C11  C12  166.38  30.0  1
 4YE  Var_09    C6   C5   N4   C3   160.47  30.0  1
 4YE  Var_10    N8   C6   C5   N4   164.79  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 4YE  chir_01  C2  C3  C1  N19  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 4YE  plan-1  C5   0.020
 4YE  plan-1  C6   0.020
 4YE  plan-1  C16  0.020
 4YE  plan-1  O7   0.020
 4YE  plan-1  N8   0.020
 4YE  plan-1  C9   0.020
 4YE  plan-2  C10  0.020
 4YE  plan-2  C11  0.020
 4YE  plan-2  C12  0.020
 4YE  plan-2  C13  0.020
 4YE  plan-2  C14  0.020
 4YE  plan-2  C15  0.020
 4YE  plan-2  C16  0.020
 4YE  plan-2  N8   0.020
 4YE  plan-2  H32  0.020
 4YE  plan-2  H33  0.020
 4YE  plan-2  H34  0.020
 4YE  plan-2  H35  0.020

